Hi Jack Monaghan,
I don't know which programmer you are using, but the configuration in the KDS is nearly the same, you should choose the according debug interface, after you connect the programmer to your board with SWD interface, then click debug, the program will download to your chip.
Here, I take PE opensda as an example:
In KDS, choose RUN-> debug configurations, then choose GDB PEMicro Interface debugging-> KL43_TEST_Debug

Choose the interface as your programmer(here is OPENSDA), then click button debug, wait the flash download finished, then your chip will be programmed.
Wish it helps you!
Any question, please contact me.
Have a great day,
Jingjing
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